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Atomistic detailed mechanism and weak cation-conducting activity of HIV-1 Vpu revealed by free energy calculations.

Padhi S, Burri RR, Jameel S, Priyakumar UD - PLoS ONE (2014)

Bottom Line: Free energy profiles corresponding to the permeation of Na+ and K+ were found to be similar to each other indicating lack of ion selection, consistent with previous experimental studies.The Ser23 residue is shown to enhance ion transport via two mechanisms: creating a weak binding site, and increasing the effective hydrophilic length of the channel, both of which have previously been hypothesized in experiments.The results are consistent with previous conductance studies that showed Vpu to be a weakly conducting ion channel.

View Article: PubMed Central - PubMed

Affiliation: Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, India.

ABSTRACT
The viral protein U (Vpu) encoded by HIV-1 has been shown to assist in the detachment of virion particles from infected cells. Vpu forms cation-specific ion channels in host cells, and has been proposed as a potential drug target. An understanding of the mechanism of ion transport through Vpu is desirable, but remains limited because of the unavailability of an experimental structure of the channel. Using a structure of the pentameric form of Vpu--modeled and validated based on available experimental data--umbrella sampling molecular dynamics simulations (cumulative simulation time of more than 0.4 µs) were employed to elucidate the energetics and the molecular mechanism of ion transport in Vpu. Free energy profiles corresponding to the permeation of Na+ and K+ were found to be similar to each other indicating lack of ion selection, consistent with previous experimental studies. The Ser23 residue is shown to enhance ion transport via two mechanisms: creating a weak binding site, and increasing the effective hydrophilic length of the channel, both of which have previously been hypothesized in experiments. A two-dimensional free energy landscape has been computed to model multiple ion permeation, based on which a mechanism for ion conduction is proposed. It is shown that only one ion can pass through the channel at a time. This, along with a stretch of hydrophobic residues in the transmembrane domain of Vpu, explains the slow kinetics of ion conduction. The results are consistent with previous conductance studies that showed Vpu to be a weakly conducting ion channel.

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Related in: MedlinePlus

Conformations with the permeating ion inside the channel.Snapshots of the Na+ ion near the ring of (A) Ser23 residues and (B) Val12 residues, respectively.
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pone-0112983-g004: Conformations with the permeating ion inside the channel.Snapshots of the Na+ ion near the ring of (A) Ser23 residues and (B) Val12 residues, respectively.

Mentions: The features of the two free energy profiles (Na+ and K+) were found to be very similar to each other. The movement of the ion into the channel from the C-terminal side is accompanied by the release of 2 kcal/mol of energy, with a shallow minimum occurring around z = −10 Å (the region is marked with an arrow in Figure 3). This corresponds to the position of the ring of Ser23 residues, and suggests the role of serine as a weak binding site. This is consistent with previous conductance studies on mutant forms of Vpu, which have proposed that the serine can act as a weak binding site for ions, since replacing the serine with a hydrophobic residue results in loss of ion channel activity. The fact that the minimum seen around the serine is shallow rather than deep indicates that the binding site is at best only a weak one. As the ion moves further into the channel, there is a surge in the free energies brought about by the unfavorable interactions that the positive ions have with the hydrophobic environment of the channel. The maximum is reached around two valine residues, namely Val9 and Val12, which occur in the middle of the hydrophobic stretch in the channel. The ions experience a soft minimum around 15 Å, which arises from the stabilization of the ion at this position by coordinating water molecules (see later). Figure 4 shows snapshots of the Na+ ion at two places inside the channel. The first snapshot shows the ion near the ring of Ser23 residues, while the second snapshot shows the ion near the ring of Val12 residues. As can be seen in the figure, the latter corresponds to the narrow stretch of the channel, where the energy barrier reaches a maximum.


Atomistic detailed mechanism and weak cation-conducting activity of HIV-1 Vpu revealed by free energy calculations.

Padhi S, Burri RR, Jameel S, Priyakumar UD - PLoS ONE (2014)

Conformations with the permeating ion inside the channel.Snapshots of the Na+ ion near the ring of (A) Ser23 residues and (B) Val12 residues, respectively.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4231112&req=5

pone-0112983-g004: Conformations with the permeating ion inside the channel.Snapshots of the Na+ ion near the ring of (A) Ser23 residues and (B) Val12 residues, respectively.
Mentions: The features of the two free energy profiles (Na+ and K+) were found to be very similar to each other. The movement of the ion into the channel from the C-terminal side is accompanied by the release of 2 kcal/mol of energy, with a shallow minimum occurring around z = −10 Å (the region is marked with an arrow in Figure 3). This corresponds to the position of the ring of Ser23 residues, and suggests the role of serine as a weak binding site. This is consistent with previous conductance studies on mutant forms of Vpu, which have proposed that the serine can act as a weak binding site for ions, since replacing the serine with a hydrophobic residue results in loss of ion channel activity. The fact that the minimum seen around the serine is shallow rather than deep indicates that the binding site is at best only a weak one. As the ion moves further into the channel, there is a surge in the free energies brought about by the unfavorable interactions that the positive ions have with the hydrophobic environment of the channel. The maximum is reached around two valine residues, namely Val9 and Val12, which occur in the middle of the hydrophobic stretch in the channel. The ions experience a soft minimum around 15 Å, which arises from the stabilization of the ion at this position by coordinating water molecules (see later). Figure 4 shows snapshots of the Na+ ion at two places inside the channel. The first snapshot shows the ion near the ring of Ser23 residues, while the second snapshot shows the ion near the ring of Val12 residues. As can be seen in the figure, the latter corresponds to the narrow stretch of the channel, where the energy barrier reaches a maximum.

Bottom Line: Free energy profiles corresponding to the permeation of Na+ and K+ were found to be similar to each other indicating lack of ion selection, consistent with previous experimental studies.The Ser23 residue is shown to enhance ion transport via two mechanisms: creating a weak binding site, and increasing the effective hydrophilic length of the channel, both of which have previously been hypothesized in experiments.The results are consistent with previous conductance studies that showed Vpu to be a weakly conducting ion channel.

View Article: PubMed Central - PubMed

Affiliation: Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, India.

ABSTRACT
The viral protein U (Vpu) encoded by HIV-1 has been shown to assist in the detachment of virion particles from infected cells. Vpu forms cation-specific ion channels in host cells, and has been proposed as a potential drug target. An understanding of the mechanism of ion transport through Vpu is desirable, but remains limited because of the unavailability of an experimental structure of the channel. Using a structure of the pentameric form of Vpu--modeled and validated based on available experimental data--umbrella sampling molecular dynamics simulations (cumulative simulation time of more than 0.4 µs) were employed to elucidate the energetics and the molecular mechanism of ion transport in Vpu. Free energy profiles corresponding to the permeation of Na+ and K+ were found to be similar to each other indicating lack of ion selection, consistent with previous experimental studies. The Ser23 residue is shown to enhance ion transport via two mechanisms: creating a weak binding site, and increasing the effective hydrophilic length of the channel, both of which have previously been hypothesized in experiments. A two-dimensional free energy landscape has been computed to model multiple ion permeation, based on which a mechanism for ion conduction is proposed. It is shown that only one ion can pass through the channel at a time. This, along with a stretch of hydrophobic residues in the transmembrane domain of Vpu, explains the slow kinetics of ion conduction. The results are consistent with previous conductance studies that showed Vpu to be a weakly conducting ion channel.

Show MeSH
Related in: MedlinePlus